Diff of the two buildlogs: -- --- b1/build.log 2023-06-06 08:55:49.803503570 +0000 +++ b2/build.log 2023-06-06 08:56:25.837924780 +0000 @@ -1,7 +1,6 @@ -W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build -I: Current time: Mon Jun 5 20:52:33 -12 2023 -I: pbuilder-time-stamp: 1686041553 +I: Current time: Tue Jul 9 05:18:48 +14 2024 +I: pbuilder-time-stamp: 1720451928 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -18,7 +17,7 @@ I: copying [./libpsortb_1.0+dfsg.orig.tar.xz] I: copying [./libpsortb_1.0+dfsg-5.debian.tar.xz] I: Extracting source -gpgv: Signature made Wed Nov 17 04:51:13 2021 -12 +gpgv: Signature made Thu Nov 18 06:51:13 2021 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -31,136 +30,169 @@ dpkg-source: info: applying use_debian_packaged_libsvm.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/9294/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/107502/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jul 9 05:18 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/107502/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/107502/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='9294' - PS1='# ' - PS2='> ' + INVOCATION_ID=ff478bd8e7cf428cae5dd4caf36606ff + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=107502 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.qjuoX3xs/pbuilderrc_8E9c --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qjuoX3xs/b1 --logfile b1/build.log libpsortb_1.0+dfsg-5.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/sbin/chroot' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.qjuoX3xs/pbuilderrc_Kluh --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qjuoX3xs/b2 --logfile b2/build.log --extrapackages usrmerge libpsortb_1.0+dfsg-5.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos2-i386 5.10.0-23-686-pae #1 SMP Debian 5.10.179-1 (2023-05-12) i686 GNU/Linux + Linux i-capture-the-hostname 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux I: ls -l /bin total 6036 - -rwxr-xr-x 1 root root 1408088 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown - -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp - -rwxr-xr-x 1 root root 136916 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 137160 Sep 20 2022 date - -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd - -rwxr-xr-x 1 root root 108940 Sep 20 2022 df - -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir - -rwxr-xr-x 1 root root 87760 Mar 22 22:20 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 34664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 84272 Mar 22 22:20 findmnt - -rwsr-xr-x 1 root root 30240 Mar 22 20:38 fusermount - -rwxr-xr-x 1 root root 218680 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 21916 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln - -rwxr-xr-x 1 root root 55600 Mar 22 23:43 login - -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls - -rwxr-xr-x 1 root root 214568 Mar 22 22:20 lsblk - -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 63016 Mar 22 22:20 more - -rwsr-xr-x 1 root root 58912 Mar 22 22:20 mount - -rwxr-xr-x 1 root root 13856 Mar 22 22:20 mountpoint - -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm - -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133224 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty - -rwsr-xr-x 1 root root 83492 Mar 22 22:20 su - -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync - -rwxr-xr-x 1 root root 598456 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch - -rwxr-xr-x 1 root root 34664 Sep 20 2022 true - -rwxr-xr-x 1 root root 17892 Mar 22 20:38 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Mar 22 22:20 umount - -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 71216 Mar 22 22:20 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/9294/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1408088 Apr 24 2023 bash + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 42920 Sep 21 2022 cat + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown + -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp + -rwxr-xr-x 1 root root 136916 Jan 6 2023 dash + -rwxr-xr-x 1 root root 137160 Sep 21 2022 date + -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd + -rwxr-xr-x 1 root root 108940 Sep 21 2022 df + -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir + -rwxr-xr-x 1 root root 87760 Mar 24 2023 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 34664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 84272 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 218680 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 21916 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln + -rwxr-xr-x 1 root root 55600 Mar 24 2023 login + -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls + -rwxr-xr-x 1 root root 214568 Mar 24 2023 lsblk + -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 63016 Mar 24 2023 more + -rwsr-xr-x 1 root root 58912 Mar 24 2023 mount + -rwxr-xr-x 1 root root 13856 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash + -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm + -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133224 Jan 6 2023 sed + lrwxrwxrwx 1 root root 9 Jul 9 05:18 sh -> /bin/bash + -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty + -rwsr-xr-x 1 root root 83492 Mar 24 2023 su + -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync + -rwxr-xr-x 1 root root 598456 Apr 7 2023 tar + -rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch + -rwxr-xr-x 1 root root 34664 Sep 21 2022 true + -rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Mar 24 2023 umount + -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 71216 Mar 24 2023 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/107502/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -246,7 +278,7 @@ Get: 38 http://deb.debian.org/debian bookworm/main i386 pkgconf-bin i386 1.8.1-1 [29.8 kB] Get: 39 http://deb.debian.org/debian bookworm/main i386 pkgconf i386 1.8.1-1 [25.9 kB] Get: 40 http://deb.debian.org/debian bookworm/main i386 pkg-config i386 1.8.1-1 [13.7 kB] -Fetched 19.6 MB in 1s (26.9 MB/s) +Fetched 19.6 MB in 0s (91.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19599 files and directories currently installed.) @@ -420,8 +452,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/libpsortb-1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libpsortb_1.0+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/107502/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/107502/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/libpsortb-1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libpsortb_1.0+dfsg-5_source.changes dpkg-buildpackage: info: source package libpsortb dpkg-buildpackage: info: source version 1.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -466,7 +509,7 @@ ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a race-free mkdir -p... /bin/mkdir -p +checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -494,10 +537,10 @@ checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking how to print strings... printf -checking for a sed that does not truncate output... /bin/sed -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E -checking for fgrep... /bin/grep -F +checking for a sed that does not truncate output... /usr/bin/sed +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E +checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B @@ -517,8 +560,8 @@ checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no -checking for a working dd... /bin/dd -checking how to truncate binary pipes... /bin/dd bs=4096 count=1 +checking for a working dd... /usr/bin/dd +checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes @@ -560,7 +603,7 @@ checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for main in -lm... yes -checking for egrep... (cached) /bin/grep -E +checking for egrep... (cached) /usr/bin/grep -E checking for float.h... yes checking for limits.h... yes checking for memory.h... yes @@ -605,19 +648,19 @@ config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build - make -j8 + make -j15 make[1]: Entering directory '/build/libpsortb-1.0+dfsg' make all-recursive make[2]: Entering directory '/build/libpsortb-1.0+dfsg' Making all in svmloc make[3]: Entering directory '/build/libpsortb-1.0+dfsg/svmloc' -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o binding.lo binding.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o svmloc.lo svmloc.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o binding.lo binding.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o svmloc.lo svmloc.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c binding.cpp -fPIC -DPIC -o .libs/binding.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c svmloc.cpp -fPIC -DPIC -o .libs/svmloc.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c binding.cpp -o binding.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c svmloc.cpp -o svmloc.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -lsvm -Wl,-z,relro -Wl,-z,now -o libsvmloc.la -rpath /usr/lib/i386-linux-gnu binding.lo svmloc.lo -lm +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -lsvm -Wl,-z,relro -Wl,-z,now -o libsvmloc.la -rpath /usr/lib/i386-linux-gnu binding.lo svmloc.lo -lm libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/12/crtbeginS.o .libs/binding.o .libs/svmloc.o -lsvm -L/usr/lib/gcc/i686-linux-gnu/12 -L/usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/12/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/12/crtendS.o /usr/lib/gcc/i686-linux-gnu/12/../../../i386-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libsvmloc.so.0 -o .libs/libsvmloc.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libsvmloc.so.0" && ln -s "libsvmloc.so.0.0.0" "libsvmloc.so.0") libtool: link: (cd ".libs" && rm -f "libsvmloc.so" && ln -s "libsvmloc.so.0.0.0" "libsvmloc.so") @@ -627,22 +670,24 @@ make[3]: Leaving directory '/build/libpsortb-1.0+dfsg/svmloc' Making all in modhmm0.92b make[3]: Entering directory '/build/libpsortb-1.0+dfsg/modhmm0.92b' -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o core_algorithms_multialpha.lo core_algorithms_multialpha.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o debug_funcs.lo debug_funcs.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hmmsearch.lo hmmsearch.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readhmm.lo readhmm.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readhmm_multialpha.lo readhmm_multialpha.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readseqs_multialpha.lo readseqs_multialpha.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o std_calculation_funcs.lo std_calculation_funcs.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o std_funcs.lo std_funcs.c -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c debug_funcs.c -fPIC -DPIC -o .libs/debug_funcs.o +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o core_algorithms_multialpha.lo core_algorithms_multialpha.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o debug_funcs.lo debug_funcs.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hmmsearch.lo hmmsearch.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readhmm.lo readhmm.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readhmm_multialpha.lo readhmm_multialpha.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readseqs_multialpha.lo readseqs_multialpha.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o std_calculation_funcs.lo std_calculation_funcs.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o std_funcs.lo std_funcs.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o training_algorithms_multialpha.lo training_algorithms_multialpha.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm_multialpha.c -fPIC -DPIC -o .libs/readhmm_multialpha.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readseqs_multialpha.c -fPIC -DPIC -o .libs/readseqs_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c core_algorithms_multialpha.c -fPIC -DPIC -o .libs/core_algorithms_multialpha.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c hmmsearch.c -fPIC -DPIC -o .libs/hmmsearch.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm.c -fPIC -DPIC -o .libs/readhmm.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c std_calculation_funcs.c -fPIC -DPIC -o .libs/std_calculation_funcs.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c debug_funcs.c -fPIC -DPIC -o .libs/debug_funcs.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c hmmsearch.c -fPIC -DPIC -o .libs/hmmsearch.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readseqs_multialpha.c -fPIC -DPIC -o .libs/readseqs_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c std_funcs.c -fPIC -DPIC -o .libs/std_funcs.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c std_calculation_funcs.c -fPIC -DPIC -o .libs/std_calculation_funcs.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c training_algorithms_multialpha.c -fPIC -DPIC -o .libs/training_algorithms_multialpha.o debug_funcs.c: In function 'dump_viterbi_path': debug_funcs.c:320:38: warning: implicit declaration of function 'get_mtx_index' [-Wimplicit-function-declaration] 320 | dump_viterbi_path(viterbi_mtxp + get_mtx_index(row-1, cur->prev, row_size), hmmp, @@ -678,80 +723,69 @@ readhmm.c:121:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] 121 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); | ^ +readhmm_multialpha.c: In function 'copy_hmm_struct': +readhmm_multialpha.c:273:34: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] + 273 | retrain_hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); + | ^ +readhmm.c: In function 'readanhmm': +readhmm.c:397:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] + 397 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); + | ^ +readhmm_multialpha.c: In function 'readhmm_multialpha': +readhmm_multialpha.c:469:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] + 469 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); + | ^ readseqs_multialpha.c: In function 'get_sequence_fasta_multi': +hmmsearch.c: In function 'get_scores': readseqs_multialpha.c:83:39: warning: assignment to 'char' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 83 | (seq_infop->seqs + seq_nr)->name[0] = "s"; | ^ +hmmsearch.c:535:19: warning: assignment to 'struct helix_site *' from incompatible pointer type 'helix_sites *' [-Wincompatible-pointer-types] + 535 | hSites->helix = (helix_sites *) malloc(sizeof (helix_sites) * helices); + | ^ readseqs_multialpha.c: In function 'get_sequence_std_multi': readseqs_multialpha.c:121:55: warning: unknown escape sequence: '\s' 121 | if(line[0] == '<' || line[0] == '#' || line[0] == '\s' || line[0] == '\n' || line[0] == '/') { | ^~~~ +hmmsearch.c: In function 'get_nullmodel_score_multi': +hmmsearch.c:656:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] + 656 | printf("Could not find letter %s when scoring null model\n", &seq[l]); + | ~^ ~~~~~~~ + | | | + | char * struct letter_s * +hmmsearch.c:674:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] + 674 | printf("Could not find letter %s when scoring null model\n", &seq_2[l]); + | ~^ ~~~~~~~~~ + | | | + | char * struct letter_s * +hmmsearch.c:693:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] + 693 | printf("Could not find letter %s when scoring null model\n", &seq_3[l]); + | ~^ ~~~~~~~~~ + | | | + | char * struct letter_s * +training_algorithms_multialpha.c: In function 'msa_baum_welch_dirichlet_multi': readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': +hmmsearch.c:712:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] + 712 | printf("Could not find letter %s when scoring null model\n", &seq[l]); + | ~^ ~~~~~~~ + | | | + | char * struct letter_s * +training_algorithms_multialpha.c:701:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 701 | alphabet = hmmp->alphabet; + | ^ +training_algorithms_multialpha.c:710:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 710 | alphabet = hmmp->alphabet_2; + | ^ readseqs_multialpha.c:372:18: warning: unknown escape sequence: '\s' 372 | else if(i == '\s' && i == '\n') { | ^~~~ -readseqs_multialpha.c:389:22: warning: implicit declaration of function 'read_multi_prior_file_multi'; did you mean 'read_prior_file_multi'? [-Wimplicit-function-declaration] - 389 | read_priorfile = read_multi_prior_file_multi(&em_di_1, hmmp, priorfile_a1, 1); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ - | read_prior_file_multi -readhmm.c: In function 'readanhmm': -readhmm.c:397:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] - 397 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); - | ^ -readhmm_multialpha.c: In function 'copy_hmm_struct': -readhmm.c: In function 'readhmm': -readhmm.c:69:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 69 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm.c: In function 'readanhmm': -readhmm.c:345:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 345 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm_multialpha.c:273:34: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] - 273 | retrain_hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); - | ^ -readhmm_multialpha.c: In function 'readhmm_multialpha': -readhmm_multialpha.c:469:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] - 469 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); - | ^ -readhmm.c: In function 'read_module': -readhmm.c:751:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 751 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm.c:786:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 786 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm.c:821:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 821 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm.c:850:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 850 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm.c:854:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 854 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readseqs_multialpha.c: In function 'get_sequence_std_multi': -readseqs_multialpha.c:286:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 286 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -readhmm.c: In function 'read_prior_files': -readhmm.c:1231:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1231 | fgets(ps, 2048, priorfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': -readseqs_multialpha.c:625:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 625 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -readseqs_multialpha.c:754:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 754 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -readseqs_multialpha.c:874:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 874 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -readseqs_multialpha.c:995:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 995 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +training_algorithms_multialpha.c:719:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 719 | alphabet = hmmp->alphabet_3; + | ^ core_algorithms_multialpha.c: In function 'msa_forward_multi': +training_algorithms_multialpha.c:728:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 728 | alphabet = hmmp->alphabet_4; + | ^ core_algorithms_multialpha.c:1192:87: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1192 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -785,6 +819,10 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +readseqs_multialpha.c:389:22: warning: implicit declaration of function 'read_multi_prior_file_multi'; did you mean 'read_prior_file_multi'? [-Wimplicit-function-declaration] + 389 | read_priorfile = read_multi_prior_file_multi(&em_di_1, hmmp, priorfile_a1, 1); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ + | read_prior_file_multi core_algorithms_multialpha.c: In function 'msa_backward_multi': core_algorithms_multialpha.c:1419:87: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1419 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); @@ -799,6 +837,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * +std_funcs.c: In function 'get_replacement_letter_index_single': funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ @@ -810,6 +849,9 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +std_funcs.c:683:62: warning: comparison between pointer and integer + 683 | if(((replacement_letters->letters + a_index)->letter)[0] == c) { + | ^~ core_algorithms_multialpha.c:1444:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1444 | a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -818,15 +860,12 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ -hmmsearch.c: In function 'get_scores': -hmmsearch.c:535:19: warning: assignment to 'struct helix_site *' from incompatible pointer type 'helix_sites *' [-Wincompatible-pointer-types] - 535 | hSites->helix = (helix_sites *) malloc(sizeof (helix_sites) * helices); - | ^ -std_funcs.c: In function 'get_replacement_letter_index_single': -std_funcs.c:683:62: warning: comparison between pointer and integer - 683 | if(((replacement_letters->letters + a_index)->letter)[0] == c) { - | ^~ +training_algorithms_multialpha.c: In function 'extended_msa_baum_welch_dirichlet_multi': +readhmm.c: In function 'readhmm': core_algorithms_multialpha.c: In function 'msa_viterbi_multi': +readhmm.c:69:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 69 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1608:87: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1608 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -835,6 +874,9 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +training_algorithms_multialpha.c:1639:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1639 | alphabet = hmmp->alphabet; + | ^ core_algorithms_multialpha.c:1615:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1615 | a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -843,6 +885,9 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +training_algorithms_multialpha.c:1646:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1646 | alphabet = hmmp->alphabet_2; + | ^ core_algorithms_multialpha.c:1624:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1624 | a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -851,6 +896,9 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +training_algorithms_multialpha.c:1653:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1653 | alphabet = hmmp->alphabet_3; + | ^ core_algorithms_multialpha.c:1633:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1633 | a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -859,31 +907,23 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ -readhmm_multialpha.c:326:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 326 | fgets(s, MAX_LINE, file); +training_algorithms_multialpha.c:1660:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1660 | alphabet = hmmp->alphabet_4; + | ^ +readhmm.c: In function 'readanhmm': +training_algorithms_multialpha.c:1784:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1784 | alphabet = hmmp->alphabet; + | ^ +readhmm.c:345:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 345 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ -hmmsearch.c: In function 'get_nullmodel_score_multi': -hmmsearch.c:656:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] - 656 | printf("Could not find letter %s when scoring null model\n", &seq[l]); - | ~^ ~~~~~~~ - | | | - | char * struct letter_s * -hmmsearch.c:674:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] - 674 | printf("Could not find letter %s when scoring null model\n", &seq_2[l]); - | ~^ ~~~~~~~~~ - | | | - | char * struct letter_s * -hmmsearch.c:693:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] - 693 | printf("Could not find letter %s when scoring null model\n", &seq_3[l]); - | ~^ ~~~~~~~~~ - | | | - | char * struct letter_s * -hmmsearch.c:712:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] - 712 | printf("Could not find letter %s when scoring null model\n", &seq[l]); - | ~^ ~~~~~~~ - | | | - | char * struct letter_s * +training_algorithms_multialpha.c:1791:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1791 | alphabet = hmmp->alphabet_2; + | ^ core_algorithms_multialpha.c: In function 'msa_one_best_multi': +training_algorithms_multialpha.c:1798:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1798 | alphabet = hmmp->alphabet_3; + | ^ core_algorithms_multialpha.c:1892:87: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1892 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -892,6 +932,9 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +training_algorithms_multialpha.c:1805:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1805 | alphabet = hmmp->alphabet_4; + | ^ core_algorithms_multialpha.c:1899:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1899 | a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -900,7 +943,10 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ -readhmm_multialpha.c: In function 'read_module_multi': +readhmm.c: In function 'read_module': +readhmm.c:751:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 751 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1908:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1908 | a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -909,23 +955,52 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ -readhmm_multialpha.c:1042:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1042 | fgets(s, MAX_LINE, file); +readhmm.c:786:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 786 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +readhmm.c:821:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 821 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1917:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1917 | a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * -readhmm_multialpha.c:1077:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1077 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +readhmm.c:850:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 850 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +readhmm.c:854:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 854 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +readhmm_multialpha.c:326:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 326 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +std_funcs.c: In function 'get_reverse_msa_seq': +readhmm.c: In function 'read_prior_files': +readhmm_multialpha.c: In function 'read_module_multi': +readhmm.c:1231:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1231 | fgets(ps, 2048, priorfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +std_funcs.c:2076:74: warning: assignment to 'int *' from 'int' makes pointer from integer without a cast [-Wint-conversion] + 2076 | *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; + | ^ +readhmm_multialpha.c:1042:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1042 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +readhmm_multialpha.c:1077:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1077 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +readseqs_multialpha.c: In function 'get_sequence_std_multi': +readseqs_multialpha.c:286:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 286 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1111:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1111 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ +std_funcs.c: In function 'get_reverse_msa_seq_multi': readhmm_multialpha.c:1140:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1140 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ @@ -935,6 +1010,9 @@ readhmm_multialpha.c:1169:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1169 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ +std_funcs.c:2184:74: warning: assignment to 'int *' from 'int' makes pointer from integer without a cast [-Wint-conversion] + 2184 | *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; + | ^ readhmm_multialpha.c:1172:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1172 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ @@ -950,87 +1028,26 @@ readhmm_multialpha.c:1236:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1236 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ -std_funcs.c: In function 'get_reverse_msa_seq': -std_funcs.c:2076:74: warning: assignment to 'int *' from 'int' makes pointer from integer without a cast [-Wint-conversion] - 2076 | *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; - | ^ -std_funcs.c: In function 'get_reverse_msa_seq_multi': -std_funcs.c:2184:74: warning: assignment to 'int *' from 'int' makes pointer from integer without a cast [-Wint-conversion] - 2184 | *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; - | ^ std_funcs.c: In function 'update_shares_prior_multi': std_funcs.c:2471:5: warning: 'return' with no value, in function returning non-void 2471 | return; | ^~~~~~ +readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': +readseqs_multialpha.c:625:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 625 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ std_funcs.c:2457:5: note: declared here 2457 | int update_shares_prior_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, | ^~~~~~~~~~~~~~~~~~~~~~~~~ -std_funcs.c: In function 'get_nr_alphabets': -std_funcs.c:2731:10: warning: 'fgets' writing 4000 bytes into a region of size 1000 overflows the destination [-Wstringop-overflow=] - 2731 | if(fgets(s, MAX_LINE, hmmfile) != NULL) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -std_funcs.c:2724:8: note: destination object 's' of size 1000 - 2724 | char s[1000]; - | ^ -In file included from /usr/include/stdio.h:906, - from std_funcs.c:1: -/usr/include/i386-linux-gnu/bits/stdio2.h:209:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' - 209 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream) - | ^~~~~ -std_funcs.c:2738:8: warning: 'fgets' writing 4000 bytes into a region of size 1000 overflows the destination [-Wstringop-overflow=] - 2738 | if(fgets(s, MAX_LINE, hmmfile) != NULL) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -std_funcs.c:2724:8: note: destination object 's' of size 1000 - 2724 | char s[1000]; - | ^ -/usr/include/i386-linux-gnu/bits/stdio2.h:209:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' - 209 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream) - | ^~~~~ -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c hmmsearch.c -o hmmsearch.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm.c -o readhmm.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c debug_funcs.c -o debug_funcs.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o training_algorithms_multialpha.lo training_algorithms_multialpha.c -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c std_calculation_funcs.c -o std_calculation_funcs.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c training_algorithms_multialpha.c -fPIC -DPIC -o .libs/training_algorithms_multialpha.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readseqs_multialpha.c -o readseqs_multialpha.o >/dev/null 2>&1 -training_algorithms_multialpha.c: In function 'msa_baum_welch_dirichlet_multi': -training_algorithms_multialpha.c:701:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 701 | alphabet = hmmp->alphabet; - | ^ -training_algorithms_multialpha.c:710:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 710 | alphabet = hmmp->alphabet_2; - | ^ -training_algorithms_multialpha.c:719:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 719 | alphabet = hmmp->alphabet_3; - | ^ -training_algorithms_multialpha.c:728:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 728 | alphabet = hmmp->alphabet_4; - | ^ -training_algorithms_multialpha.c: In function 'extended_msa_baum_welch_dirichlet_multi': -training_algorithms_multialpha.c:1639:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1639 | alphabet = hmmp->alphabet; - | ^ -training_algorithms_multialpha.c:1646:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1646 | alphabet = hmmp->alphabet_2; - | ^ -training_algorithms_multialpha.c:1653:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1653 | alphabet = hmmp->alphabet_3; - | ^ -training_algorithms_multialpha.c:1660:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1660 | alphabet = hmmp->alphabet_4; - | ^ -training_algorithms_multialpha.c:1784:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1784 | alphabet = hmmp->alphabet; - | ^ -training_algorithms_multialpha.c:1791:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1791 | alphabet = hmmp->alphabet_2; - | ^ -training_algorithms_multialpha.c:1798:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1798 | alphabet = hmmp->alphabet_3; - | ^ -training_algorithms_multialpha.c:1805:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1805 | alphabet = hmmp->alphabet_4; - | ^ +readseqs_multialpha.c:754:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 754 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +readseqs_multialpha.c:874:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 874 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +readseqs_multialpha.c:995:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 995 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c: In function 'add_to_E_multi': training_algorithms_multialpha.c:3564:5: warning: implicit declaration of function 'add_to_E_continuous' [-Wimplicit-function-declaration] 3564 | add_to_E_continuous(E, Eka_base, msa_seq, p, k, a_size, emissions); @@ -1068,7 +1085,33 @@ funcs.h:240:102: note: expected 'char *' but argument is of type 'int' 240 | int k, int a_size, int normalize, double *subst_mtx, char *alphabet); | ~~~~~~^~~~~~~~ +std_funcs.c: In function 'get_nr_alphabets': +std_funcs.c:2731:10: warning: 'fgets' writing 4000 bytes into a region of size 1000 overflows the destination [-Wstringop-overflow=] + 2731 | if(fgets(s, MAX_LINE, hmmfile) != NULL) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +std_funcs.c:2724:8: note: destination object 's' of size 1000 + 2724 | char s[1000]; + | ^ +In file included from /usr/include/stdio.h:906, + from std_funcs.c:1: +/usr/include/i386-linux-gnu/bits/stdio2.h:209:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' + 209 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream) + | ^~~~~ +std_funcs.c:2738:8: warning: 'fgets' writing 4000 bytes into a region of size 1000 overflows the destination [-Wstringop-overflow=] + 2738 | if(fgets(s, MAX_LINE, hmmfile) != NULL) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +std_funcs.c:2724:8: note: destination object 's' of size 1000 + 2724 | char s[1000]; + | ^ +/usr/include/i386-linux-gnu/bits/stdio2.h:209:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' + 209 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream) + | ^~~~~ +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c hmmsearch.c -o hmmsearch.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm.c -o readhmm.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c debug_funcs.c -o debug_funcs.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c std_calculation_funcs.c -o std_calculation_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm_multialpha.c -o readhmm_multialpha.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readseqs_multialpha.c -o readseqs_multialpha.o >/dev/null 2>&1 In function 'fgets', inlined from 'get_nr_alphabets' at std_funcs.c:2731:10: /usr/include/i386-linux-gnu/bits/stdio2.h:215:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] @@ -1082,7 +1125,7 @@ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c std_funcs.c -o std_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c core_algorithms_multialpha.c -o core_algorithms_multialpha.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c training_algorithms_multialpha.c -o training_algorithms_multialpha.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -Wl,-z,relro -Wl,-z,now -o libmodhmm.la -rpath /usr/lib/i386-linux-gnu core_algorithms_multialpha.lo debug_funcs.lo hmmsearch.lo readhmm.lo readhmm_multialpha.lo readseqs_multialpha.lo std_calculation_funcs.lo std_funcs.lo training_algorithms_multialpha.lo -lm +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -Wl,-z,relro -Wl,-z,now -o libmodhmm.la -rpath /usr/lib/i386-linux-gnu core_algorithms_multialpha.lo debug_funcs.lo hmmsearch.lo readhmm.lo readhmm_multialpha.lo readseqs_multialpha.lo std_calculation_funcs.lo std_funcs.lo training_algorithms_multialpha.lo -lm libtool: link: gcc -shared -fPIC -DPIC .libs/core_algorithms_multialpha.o .libs/debug_funcs.o .libs/hmmsearch.o .libs/readhmm.o .libs/readhmm_multialpha.o .libs/readseqs_multialpha.o .libs/std_calculation_funcs.o .libs/std_funcs.o .libs/training_algorithms_multialpha.o -lm -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libmodhmm.so.0 -o .libs/libmodhmm.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libmodhmm.so.0" && ln -s "libmodhmm.so.0.0.0" "libmodhmm.so.0") libtool: link: (cd ".libs" && rm -f "libmodhmm.so" && ln -s "libmodhmm.so.0.0.0" "libmodhmm.so") @@ -1095,7 +1138,7 @@ make[2]: Leaving directory '/build/libpsortb-1.0+dfsg' make[1]: Leaving directory '/build/libpsortb-1.0+dfsg' dh_auto_test - make -j8 check "TESTSUITEFLAGS=-j8 --verbose" VERBOSE=1 + make -j15 check "TESTSUITEFLAGS=-j15 --verbose" VERBOSE=1 make[1]: Entering directory '/build/libpsortb-1.0+dfsg' Making check in svmloc make[2]: Entering directory '/build/libpsortb-1.0+dfsg/svmloc' @@ -1118,8 +1161,8 @@ Making install in svmloc make[3]: Entering directory '/build/libpsortb-1.0+dfsg/svmloc' make[4]: Entering directory '/build/libpsortb-1.0+dfsg/svmloc' - /bin/mkdir -p '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libsvmloc.la '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' + /usr/bin/mkdir -p '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libsvmloc.la '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libsvmloc.so.0.0.0 /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libsvmloc.so.0.0.0 libtool: install: (cd /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libsvmloc.so.0.0.0 libsvmloc.so.0 || { rm -f libsvmloc.so.0 && ln -s libsvmloc.so.0.0.0 libsvmloc.so.0; }; }) libtool: install: (cd /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libsvmloc.so.0.0.0 libsvmloc.so || { rm -f libsvmloc.so && ln -s libsvmloc.so.0.0.0 libsvmloc.so; }; }) @@ -1134,8 +1177,8 @@ Making install in modhmm0.92b make[3]: Entering directory '/build/libpsortb-1.0+dfsg/modhmm0.92b' make[4]: Entering directory '/build/libpsortb-1.0+dfsg/modhmm0.92b' - /bin/mkdir -p '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libmodhmm.la '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' + /usr/bin/mkdir -p '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libmodhmm.la '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libmodhmm.so.0.0.0 /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libmodhmm.so.0.0.0 libtool: install: (cd /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libmodhmm.so.0.0.0 libmodhmm.so.0 || { rm -f libmodhmm.so.0 && ln -s libmodhmm.so.0.0.0 libmodhmm.so.0; }; }) libtool: install: (cd /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libmodhmm.so.0.0.0 libmodhmm.so || { rm -f libmodhmm.so && ln -s libmodhmm.so.0.0.0 libmodhmm.so; }; }) @@ -1203,12 +1246,12 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libsvmloc0' in '../libsvmloc0_1.0+dfsg-5_i386.deb'. -dpkg-deb: building package 'libmodhmm-dev' in '../libmodhmm-dev_1.0+dfsg-5_i386.deb'. -dpkg-deb: building package 'libmodhmm0-dbgsym' in '../libmodhmm0-dbgsym_1.0+dfsg-5_i386.deb'. -dpkg-deb: building package 'libsvmloc-dev' in '../libsvmloc-dev_1.0+dfsg-5_i386.deb'. dpkg-deb: building package 'libmodhmm0' in '../libmodhmm0_1.0+dfsg-5_i386.deb'. +dpkg-deb: building package 'libmodhmm0-dbgsym' in '../libmodhmm0-dbgsym_1.0+dfsg-5_i386.deb'. +dpkg-deb: building package 'libmodhmm-dev' in '../libmodhmm-dev_1.0+dfsg-5_i386.deb'. +dpkg-deb: building package 'libsvmloc0' in '../libsvmloc0_1.0+dfsg-5_i386.deb'. dpkg-deb: building package 'libsvmloc0-dbgsym' in '../libsvmloc0-dbgsym_1.0+dfsg-5_i386.deb'. +dpkg-deb: building package 'libsvmloc-dev' in '../libsvmloc-dev_1.0+dfsg-5_i386.deb'. dpkg-genbuildinfo --build=binary -O../libpsortb_1.0+dfsg-5_i386.buildinfo dpkg-genchanges --build=binary -O../libpsortb_1.0+dfsg-5_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1216,12 +1259,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/107502/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/107502/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/9294 and its subdirectories -I: Current time: Mon Jun 5 20:55:49 -12 2023 -I: pbuilder-time-stamp: 1686041749 +I: removing directory /srv/workspace/pbuilder/107502 and its subdirectories +I: Current time: Tue Jul 9 05:19:22 +14 2024 +I: pbuilder-time-stamp: 1720451962